THE recent agreement between the United States and Russia on Syria’s chemical weapons made clear what should have been obvious long ago: President Obama’s effort to uphold international norms against weapons of mass destruction in the Middle East will entangle the United States in a diplomatic and strategic maze that is about much more than Syria’s chemical arsenal.

President Bashar al-Assad of Syria insists that the purpose of his chemical arsenal was always to deter Israel’s nuclear weapons. If Syria actually disarms, what about Egypt and Israel? Egypt (about whose chemical weapons the United States has been strangely silent) points to Israel. And Israel of course has its own chemical weapons to deter Syria’s and Egypt’s, and it is not about to give them up. A headline in the Israeli daily Haaretz a few days ago stated: “Israel adamant it won’t ratify chemical arms treaty before hostile neighbors.”

These three countries have not adhered to the Biological Weapons Convention either. And Israel is not a member of the Nuclear Nonproliferation Treaty, despite having developed a formidable nuclear arsenal of its own, which will soon become the central fact in this drama, whether the United States likes it or not.

An obstacle of America’s own making has long prevented comprehensive negotiations over weapons of mass destruction in the Middle East. While the world endlessly discusses Iran’s nuclear capabilities and the likelihood that it will succeed in developing an atomic arsenal, hardly anyone in the United States ever mentions Israel’s nuclear weapons.

Mr. Obama, like his predecessors, pretends that he doesn’t know anything about them. This taboo impedes discussions within Washington and internationally. It has kept America from pressing Egypt and Syria to ratify the chemical and biological weapons conventions. Doing so would have brought immediate objections about American acceptance of Israel’s nuclear weapons.

What sustains this pretense is the myth that America is locked into covering up Israeli nuclear bombs because of a 1969 agreement between President Richard M. Nixon and Israel’s prime minister, Golda Meir. For Mr. Nixon, it was mainly about gaining Israeli support in the cold war. He and Mrs. Meir understood the need to discourage the Soviets from providing their Arab allies with nuclear weapons. A declared Israeli nuclear arsenal would have led to pressure for Moscow to do so. But such cold war reasons for America to stay mum evaporated decades ago. Everyone knows the Israelis have nuclear bombs. Today, the main effect of the ambiguity is to prevent serious regional arms-control negotiations.

All other countries in the region are members of the nonproliferation treaty, but there are still unresolved issues. Syria was caught building an illicit nuclear reactor in 2007, which Israel swiftly bombed. Mr. Assad still has not allowed international inspectors to fully investigate that obliterated reactor site. And Syria’s ally Iran is suspected of trying to assemble its own weapons program to challenge Israel’s nuclear monopoly. Indeed, many analysts believed that Mr. Obama’s decision to issue a “red line” barring the use of chemical weapons in Syria was in fact driven by the perceived need to demonstrate that he was prepared to use force against Iran if it moved further toward nuclear weapons.

This witches’ brew was supposed to become the subject of an international conference, mandated in 2010 by the unanimous vote of the members of the nonproliferation treaty, including the United States. But that conference hasn’t happened, in part because of White House ambivalence about how it might affect Israel.

In April, the American assistant secretary of state for international security and nonproliferation, Thomas M. Countryman, expressed hope that the conference would be held by this fall. And earlier this month, Russia’s foreign minister, Sergey V. Lavrov, urged all parties to set a conference date “as quickly as possible.” He also argued that it should include Israel and Iran. Russia attempted to include the conference in last week’s agreement, but Secretary of State John Kerry resisted. It is not going to go away.

If Washington wants negotiations over weapons of mass destruction in the Middle East to work — or even just to avoid making America appear ridiculous — Mr. Obama should begin by being candid. He cannot expect the countries participating in a conference to take America seriously if the White House continues to pretend that we don’t know whether Israel has nuclear weapons, or for that matter whether Egypt and Israel have chemical or biological ones.

And if Israel’s policy on the subject is so frozen that it is unable to come clean, Mr. Obama must let the United States government be honest about Israel’s arsenal and act on those facts, for both America’s good and Israel’s.